Ligand profile

U13

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 2gg3 UniProt P0AE18 Formula C₉H₇FN₆
Mol. weight 218.20 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
U13
PDB
2gg3
UniProt (similar protein)
P0AE18
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 218.20 Da
LogP (Crippen) 2.48
H-bond donors 2
H-bond acceptors 5
TPSA 99.31 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 16
Fraction sp³ C 0.00
Formula C₉H₇FN₆

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 99.3
  • −1 ≤ LogP ≤ 5 2.48
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 218.2
  • LogP ≤ 5 2.48
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 99.3
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C/1\C(=C(N=N1)N)/N=N/c2ccc(cc2)F
InChI 
InChI=1S/C9H7FN6/c10-5-1-3-6(4-2-5)13-14-7-8(11)15-16-9(7)12/h1-4,11H,12H2/b11-8+,14-13+
InChIKey 
HALOLQDLOLYIOW-ZOBWXTBZSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00557

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2384.

PDB 45

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)